private DataTable GetDataTable(int timeout, int?topX)
{
var qb = new QueryBuilder("distinct", null);
if (topX != null)
{
qb.TopX = topX.Value;
}
qb.AddColumn(_extractionInformation);
var server = _extractionInformation.CatalogueItem.Catalogue.GetDistinctLiveDatabaseServer(DataAccessContext.DataExport, true);
var colName = _extractionInformation.GetRuntimeName();
DataTable dt = new DataTable();
dt.Columns.Add(colName);
using (var con = server.GetConnection())
{
con.Open();
var cmd = server.GetCommand(qb.SQL, con);
cmd.CommandTimeout = timeout;
var r = cmd.ExecuteReader();
while (r.Read())
{
dt.Rows.Add(new[] { r[colName] });
}
}
return(dt);
}
/// <inheritdoc/>
public override void Execute()
{
base.Execute();
foreach (var descCol in _lookupDescriptionColumns)
{
Lookup lookup = new Lookup(_catalogueRepository, descCol, _fkToPkTuples.First().Item1, _fkToPkTuples.First().Item2, ExtractionJoinType.Left, _collation);
foreach (var supplementalKeyPair in _fkToPkTuples.Skip(1))
{
new LookupCompositeJoinInfo(_catalogueRepository, lookup, supplementalKeyPair.Item1, supplementalKeyPair.Item2, _collation);
}
if (_alsoCreateExtractionInformations)
{
string proposedName;
if (_lookupDescriptionColumns.Length == 1)
{
proposedName = _foreignKeyExtractionInformation.GetRuntimeName() + "_Desc";
}
else
{
proposedName = _foreignKeyExtractionInformation.GetRuntimeName() + "_" + descCol.GetRuntimeName();
}
var newCatalogueItem = new CatalogueItem(_catalogueRepository, _catalogue, proposedName);
newCatalogueItem.SetColumnInfo(descCol);
//bump everyone down 1
foreach (var toBumpDown in _allExtractionInformations.Where(e => e.Order > _foreignKeyExtractionInformation.Order))
{
toBumpDown.Order++;
toBumpDown.SaveToDatabase();
}
var newExtractionInformation = new ExtractionInformation(_catalogueRepository, newCatalogueItem, descCol, descCol.ToString());
newExtractionInformation.ExtractionCategory = ExtractionCategory.Supplemental;
newExtractionInformation.Alias = newCatalogueItem.Name;
newExtractionInformation.Order = _foreignKeyExtractionInformation.Order + 1;
newExtractionInformation.SaveToDatabase();
}
}
_catalogue.ClearAllInjections();
}
public override void Execute()
{
if (_extractionIdentifierColumn == null)
{
var cata = SelectOne(Activator.RepositoryLocator.CatalogueRepository.GetAllObjects <Catalogue>());
if (cata == null)
{
return;
}
SetExtractionIdentifierColumn(GetExtractionInformationFromCatalogue(cata));
}
base.Execute();
var request = GetCohortCreationRequest("All patient identifiers in ExtractionInformation '" + _extractionIdentifierColumn.CatalogueItem.Catalogue + "." + _extractionIdentifierColumn.GetRuntimeName() + "' (ID=" + _extractionIdentifierColumn.ID + ")");
//user choose to cancel the cohort creation request dialogue
if (request == null)
{
return;
}
request.ExtractionIdentifierColumn = _extractionIdentifierColumn;
var configureAndExecute = GetConfigureAndExecuteControl(request, "Import column " + _extractionIdentifierColumn + " as cohort and commmit results");
Activator.ShowWindow(configureAndExecute);
}
public bool IsCompatible(ExtractionInformation extractionInformation)
{
return(extractionInformation.GetRuntimeName() == RuntimeName && extractionInformation.ColumnInfo.Data_type == DataType);
}
public PrivateIdentifierPrototype(ExtractionInformation extractionInformation)
{
RuntimeName = extractionInformation.GetRuntimeName();
DataType = extractionInformation.ColumnInfo.Data_type;
MatchingExtractionInformations = new List <ExtractionInformation>(new [] { extractionInformation });
}
public void TestActuallyCreatingIt(DatabaseType type)
{
var db = GetCleanedServer(type);
//drop it
db.Drop();
CreateNewCohortDatabaseWizard wizard = new CreateNewCohortDatabaseWizard(db, CatalogueRepository, DataExportRepository, false);
_extractionInfo2.IsExtractionIdentifier = true;
_extractionInfo2.SaveToDatabase();
var candidate = wizard.GetPrivateIdentifierCandidates().Single(c => c.RuntimeName.Equals("PrivateIdentifierB"));
var ect = wizard.CreateDatabase(
candidate,
new ThrowImmediatelyCheckNotifier());
//database should exist
DiscoveredServerICanCreateRandomDatabasesAndTablesOn.ExpectDatabase(cohortDatabaseName);
Assert.IsTrue(db.Exists());
//did it create the correct type?
Assert.AreEqual(type, ect.DatabaseType);
//the ExternalCohortTable should pass tests
ect.Check(new ThrowImmediatelyCheckNotifier());
//now try putting someone in it
//the project it will go under
var project = new Project(DataExportRepository, "MyProject");
project.ProjectNumber = 10;
project.SaveToDatabase();
//the request to put it under there
var request = new CohortCreationRequest(project, new CohortDefinition(null, "My cohort", 1, 10, ect), DataExportRepository, "Blah");
//the actual cohort data
DataTable dt = new DataTable();
dt.Columns.Add(_extractionInfo2.GetRuntimeName());
dt.Rows.Add(101243); //_extractionInfo2 is of type int
//the destination component that will put it there
var dest = new BasicCohortDestination();
dest.PreInitialize(request, new ThrowImmediatelyDataLoadEventListener());
//tell it to use the guid allocator
dest.ReleaseIdentifierAllocator = typeof(GuidReleaseIdentifierAllocator);
dest.ProcessPipelineData(dt, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
dest.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
var cohort = request.CohortCreatedIfAny;
Assert.IsNotNull(cohort);
var externalData = cohort.GetExternalData();
Assert.AreEqual(10, externalData.ExternalProjectNumber);
Assert.IsFalse(string.IsNullOrEmpty(externalData.ExternalDescription));
Assert.AreEqual(DateTime.Now.Year, externalData.ExternalCohortCreationDate.Value.Year);
Assert.AreEqual(DateTime.Now.Month, externalData.ExternalCohortCreationDate.Value.Month);
Assert.AreEqual(DateTime.Now.Day, externalData.ExternalCohortCreationDate.Value.Day);
Assert.AreEqual(DateTime.Now.Hour, externalData.ExternalCohortCreationDate.Value.Hour);
cohort.AppendToAuditLog("Test");
Assert.IsTrue(cohort.AuditLog.Contains("Test"));
Assert.AreEqual(1, cohort.Count);
Assert.AreEqual(1, cohort.CountDistinct);
var cohortTable = cohort.FetchEntireCohort();
Assert.AreEqual(1, cohortTable.Rows.Count);
var helper = ect.GetQuerySyntaxHelper();
Assert.AreEqual(101243, cohortTable.Rows[0][helper.GetRuntimeName(ect.PrivateIdentifierField)]);
var aguid = cohortTable.Rows[0][helper.GetRuntimeName(ect.ReleaseIdentifierField)].ToString();
Assert.IsFalse(string.IsNullOrWhiteSpace(aguid)); //should be a guid
//test reversing the anonymisation of something
var dtAno = new DataTable();
dtAno.Columns.Add(cohort.GetReleaseIdentifier(true));
dtAno.Columns.Add("Age");
dtAno.Rows.Add(aguid, 23);
dtAno.Rows.Add(aguid, 99);
cohort.ReverseAnonymiseDataTable(dtAno, new ThrowImmediatelyDataLoadEventListener(), true);
Assert.AreEqual(2, dtAno.Columns.Count);
Assert.IsTrue(dtAno.Columns.Contains(cohort.GetPrivateIdentifier(true)));
Assert.AreEqual("101243", dtAno.Rows[0][cohort.GetPrivateIdentifier(true)]);
Assert.AreEqual("101243", dtAno.Rows[1][cohort.GetPrivateIdentifier(true)]);
}
/// <summary>
/// Returns a human readable description recording that an <see cref="ExtractableCohort"/>
/// was generated by fetching identifiers from the given column <paramref name="extractionIdentifierColumn"/>
/// </summary>
/// <param name="extractionIdentifierColumn"></param>
/// <returns></returns>
public string GetDescription(ExtractionInformation extractionIdentifierColumn)
{
return(InExtractionInformation + " '" + extractionIdentifierColumn.CatalogueItem.Catalogue + "." + extractionIdentifierColumn.GetRuntimeName() + "' (ID=" + extractionIdentifierColumn.ID + ")");
}
